I've been told my BMW mechanics to think of the N55 as a cost reduced version of the N54. BMW simplified the design, cut out some of the high end components (i.e. piezo fuel injectors, dual independent turbos) and traded off raw performance for ability to better control fuel consumption.

N55 still uses HPFP, but design has been improved. N54's with latest HPFP should no longer experience high failure rates. My E90 MSport is still on its original fuel pump. The 2010 DME reprogram is said to address this issue.

The N54 was/is one heck of an engine. I had one in my 135i.
Look at enough dyno's of early N54's, later N54's, and N55's and you soon see that there is VERY little difference in maximum HP and torque output.
Some will show the N55 producing more torque, some showing the N54 producing more HP.
There appears to be as much variance between N54 engines as there is between N54 and N55 engines.
It's a wash.
Biggest, or at least most noticeable difference, is in throttle response, fuel economy, and emissions, which favor the N55, tuning potential goes to the N54.
I don't see the N54 as having more "raw" performance, it's simply not proven stock for stock.

My 135i N54 was very nice, strong.
In my 335i the N55 in conjunction with the whole different drive line feels stronger and smoother to me, not that the N54 wasn't smooth.
I'm just comparing how the whole car responds to throttle input.
My N54 had awful throttle response, again, mostly due to BMW's tinkering to "correct" things. My 135i started with decent throttle response, and after a software update that was supposed to address long cranks and potential HPFP issues, throttle response was gone.
My 335i's throttle response is excellent. "Comfort" has better response than my 135i did, and "sport" really sharpens it and I really prefer "sport" mode throttle response.

As for the whole "lower cost version", BMW designed the N55 to be more cost effective to build, but that doesn't mean it's a "lower cost", meaning lesser", engine.

Compared to the N54 the N55 has MORE advanced technology, not simplified.
The N55 uses a twin scroll turbo, which is a more advanced turbo design made to operate with greater efficiency across a broader rpm range.
To do that it uses a more advanced manifold that can flow to the lower rpm side of the twin scroll and then to the higher rpm side.

Also the N55 includes valvetronic, which controls valve lift, and it responds quicker to throttle input. With valvetronic the engine doesn't require a throttle plate to control air flow to the cylinders, that's done by VT controlling intake valve openings
Valvetronic is much more advanced technology than the N54's traditional throttle plate and valve control.

The N55 is actually a very modern turbo engine design, being the first BMW engine to couple turbocharging with valvetronic intake control.
With all the modern technology put into the N55 it is more fuel efficient and produces lower emissions compared to the N54.
Does it cost less for BMW to build? BMW say it does.
But that's an advancement, a positive not a negative.